Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis, Current Opinion in Biotechnology, vol.23, issue.1, pp.9-15, 2012. ,
DOI : 10.1016/j.copbio.2011.11.013
Value of a newly sequenced bacterial genome, World J Biol Chem, vol.5, issue.2, pp.161-169, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01209663
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs, Genome Research, vol.18, issue.5, pp.821-830, 2008. ,
DOI : 10.1101/gr.074492.107
Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler, PLoS ONE, vol.4, issue.12, p.8407, 2009. ,
DOI : 10.1371/journal.pone.0008407.s001
Unlocking Short Read Sequencing for Metagenomics, PLoS ONE, vol.17, issue.5, p.11840, 2010. ,
DOI : 10.1371/journal.pone.0011840.s001
Generation of Long Insert Pairs Using a Cre-LoxP Inverse PCR Approach, PLoS ONE, vol.5, issue.1, p.29437, 2012. ,
DOI : 10.1371/journal.pone.0029437.s006
NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries, Bioinformatics, vol.30, issue.4, pp.566-574, 2014. ,
DOI : 10.1093/bioinformatics/btt702
Scaffolding pre-assembled contigs using SSPACE, Bioinformatics, vol.27, issue.4, pp.578-587, 2011. ,
DOI : 10.1093/bioinformatics/btq683
SOPRA: Scaffolding algorithm for paired reads via statistical optimization, BMC Bioinformatics, vol.11, issue.1, p.345, 2010. ,
DOI : 10.1186/1471-2105-11-345
Fast scaffolding with small independent mixed integer programs, Bioinformatics, vol.27, issue.23, pp.3259-65, 2011. ,
DOI : 10.1093/bioinformatics/btr562
SCARPA: scaffolding reads with practical algorithms, Bioinformatics, vol.29, issue.4, pp.428-462, 2013. ,
DOI : 10.1093/bioinformatics/bts716
A comprehensive evaluation of assembly scaffolding tools, Genome Biology, vol.15, issue.3, p.42, 2014. ,
DOI : 10.1186/gb-2004-5-2-r12
GAGE: A critical evaluation of genome assemblies and assembly algorithms, Genome Research, vol.22, issue.3, pp.557-67, 2012. ,
DOI : 10.1101/gr.131383.111
QUAST: quality assessment tool for genome assemblies, Bioinformatics, vol.29, issue.8, pp.1072-1077, 2013. ,
DOI : 10.1093/bioinformatics/btt086
Bambus 2: scaffolding metagenomes, Bioinformatics, vol.27, issue.21, pp.2964-71, 2011. ,
DOI : 10.1093/bioinformatics/btr520
Aggressive assembly of pyrosequencing reads with mates, Bioinformatics, vol.24, issue.24, pp.2818-2842, 2008. ,
DOI : 10.1093/bioinformatics/btn548
SwmB, a 1.12-Megadalton Protein That Is Required for Nonflagellar Swimming Motility in Synechococcus, Journal of Bacteriology, vol.189, issue.3, pp.1158-62, 2007. ,
DOI : 10.1128/JB.01500-06
ABACAS: algorithm-based automatic contiguation of assembled sequences, Bioinformatics, vol.25, issue.15, pp.1968-1977, 2009. ,
DOI : 10.1093/bioinformatics/btp347
Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps, Genome Biology, vol.11, issue.4, p.41, 2010. ,
DOI : 10.1186/gb-2010-11-4-r41
Toward almost closed genomes with GapFiller, Genome Biology, vol.13, issue.6, p.56, 2012. ,
DOI : 10.1186/gb-2009-10-10-r103
Finishing genomes with limited resources: lessons from an ensemble of microbial genomes, BMC Genomics, vol.11, issue.1, p.242, 2010. ,
DOI : 10.1186/1471-2164-11-242
Scaffolder - software for manual genome scaffolding, Source Code for Biology and Medicine, vol.7, issue.1, p.4, 2012. ,
DOI : 10.1093/bioinformatics/btq475
Genomer ??? A Swiss Army Knife for Genome Scaffolding, PLoS ONE, vol.34, issue.6, p.66922, 2013. ,
DOI : 10.1371/journal.pone.0066922
Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology, Bioinformatics, vol.26, issue.14, pp.1704-1711, 2010. ,
DOI : 10.1093/bioinformatics/btq269
Function and evolution of the psbA gene family in marine Synechococcus: Synechococcus sp. WH7803 as a case study, The ISME Journal, vol.109, issue.9, pp.937-53, 2008. ,
DOI : 10.1111/j.1462-2920.2005.00833.x
URL : https://hal.archives-ouvertes.fr/hal-00338642
EULER-PCR: FINISHING EXPERIMENTS FOR REPEAT RESOLUTION, Biocomputing 2002, pp.199-210, 2002. ,
DOI : 10.1142/9789812799623_0019
An algorithm for automated closure during assembly, BMC Bioinformatics, vol.11, issue.1, p.11, 2010. ,
DOI : 10.1186/1471-2105-11-457
The genome of a motile marine Synechococcus, Nature, vol.424, issue.6952, pp.1037-1079, 2003. ,
DOI : 10.1038/nature01943
Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota, Science, vol.335, issue.6068, pp.587-90, 2012. ,
DOI : 10.1126/science.1212665
BLAST: at the core of a powerful and diverse set of sequence analysis tools, Nucleic Acids Research, vol.32, issue.Web Server, pp.20-25, 2004. ,
DOI : 10.1093/nar/gkh435
Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-366 ,
DOI : 10.1093/bioinformatics/btp352
The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2087, 2009. ,
DOI : 10.1093/bioinformatics/btp352
Using MUMmer to Identify Similar Regions in Large Sequence Sets, Curr Protoc Bioinformatics, vol.291, issue.10, p.13, 2003. ,
DOI : 10.1002/0471250953.bi1003s00